Otto Warburg International Summer School and Workshop on Networks and Regulation

The Otto Warburg International Summer School and Workshop on Networks and Regulation

Authors: Peter F Arndt and Martin Vingron

Transcriptional regulation at a glance

Considering that 80 genomes have been sequenced, providing us with the static information of the genome, it is still a long way to reveal the relationship between complex genotypes and phenotypes. The transcri...

Authors: Silke Sperling

Computational analyses of eukaryotic promoters

Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverse-engineering gene regulatio...

Authors: Michael Q Zhang

Finding regulatory elements and regulatory motifs: a general probabilistic framework

Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding specificities of regulator...

Authors: Erik van Nimwegen

Inferring cellular networks – a review

In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used method...

Authors: Florian Markowetz and Rainer Spang

Dissecting complex transcriptional responses using pathway-level scores based on prior information

The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cel...

Authors: Harmen J Bussemaker, Lucas D Ward and Andre Boorsma

From biophysics to evolutionary genetics: statistical aspects of gene regulation

This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by...

Authors: Michael Lässig

Graphs in molecular biology

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of applica...

Authors: Wolfgang Huber, Vincent J Carey, Li Long, Seth Falcon and Robert Gentleman

Current approaches to gene regulatory network modelling

Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology mode...

Authors: Thomas Schlitt and Alvis Brazma